It often happens that I spend a lot of time writing high-quality, working answers, to which I expect reputation increase.

Some OPs, instead of accepting the answer or upvoting it, write a thanks, it worked or similar comments. It seems that every response to this behavior is wrong somehow:

Ask for an upvote/accept in a response comment: conversational comment. Also, gives a fishing for likes atmosphere to this wonderful website. The thing I do most often, but I want to avoid it as much as possible.

Flag the thank you comment as conversational: in my opinion, conflicts with welcoming new users. Also, same drawbacks as the following:

Do nothing: Doesn't conflict with anything, but the thanking user is likely to re-do the same mistake. Also, I don't get any reputation increase for my work, which is not rewarding and kind of unfair, and pushes me to lower my answering efforts.

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Also remember that some users can't upvote because they don't have at least 15 reputation.
– Modus TollensJan 8 at 14:08

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Don't dwell on the OP response to your answers too much. Whether your goal is to improve the Q&A library, to play the reputation game, or some combination of those, it's a long-term goal. If, as you say, you spend a lot of time writing high-quality, working answers, you'll achieve it. A few people here and there who don't understand the system won't make much difference.
– Don't PanicJan 8 at 15:58

1 Answer
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Do nothing. Users are free to vote and accept answers as they see fit and you can still get votes on your answers from other users. In the end them upvoting and accepting your answer just gives you imaginary points on an internet website.

You could flag the comment as unneeded as thank you comments don't do anything to help the answer and comments are not permanent but that does not impact the overall point of just moving on if they didn't vote/accept on your answer.